public static string GetHeader(IndexedElement element, CVParam param) { StringBuilder sb = new StringBuilder(); sb.Append(OPT).Append("_").Append(element == null ? GLOBAL : element.Reference); sb.Append("_").Append(CV).Append(param.Accession).Append("_").Append(param.Name.Replace(" ", "_")); return sb.ToString(); }
private void addPeptideValue() { MsRun msRun1 = new MsRun(1); Assay assay1 = new Assay(1); Assay assay2 = new Assay(2); StudyVariable studyVariable1 = new StudyVariable(1); MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Peptide_Header); factory.AddOptionalColumn(PeptideColumn.SEARCH_ENGINE_SCORE, msRun1); factory.AddAbundanceOptionalColumn(assay1); factory.AddAbundanceOptionalColumn(studyVariable1); factory.AddAbundanceOptionalColumn(assay2); factory.AddOptionalColumn(msRun1, "my_value", typeof (string)); CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null); factory.AddOptionalColumn(param, typeof (string)); Metadata metadata = new Metadata(); metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file")); Console.WriteLine(factory); Peptide peptide = new Peptide(factory, metadata); peptide.Sequence = "KVPQVSTPTLVEVSR"; peptide.Accession = "P02768"; peptide.SetUnique("0"); peptide.Database = "UniProtKB"; peptide.DatabaseVersion = "2011_11"; peptide.SetSearchEngine("[MS,MS:1001207,Mascot,]|[MS,MS:1001208,Sequest,]"); peptide.SetBestSearchEngineScore("[MS,MS:1001155,Sequest:xcorr,2]"); peptide.Reliability = Reliability.findReliability("3"); peptide.SetModifications( "3[MS,MS:1001876, modification probability, 0.8]|4[MS,MS:1001876, modification probability, 0.2]-MOD:00412,8[MS,MS:1001876, modification probability, 0.3]-MOD:00412"); peptide.AddRetentionTime(10.2); peptide.AddRetentionTimeWindow(1123.2); peptide.AddRetentionTimeWindow(1145.3); peptide.Charge = new Integer(2); peptide.MassToCharge = 1234.4; peptide.URI = new Uri("http://www.ebi.ac.uk/pride/link/to/peptide"); peptide.SetSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9"); Console.WriteLine(peptide); }
public bool addSearchEngineScore(MsRun msRun, CVParam param) { if (param == null){ return false; } SplitList<Param> paramList = getSearchEngineScore(msRun); if (paramList == null){ paramList = new SplitList<Param>(MZTabConstants.BAR); setSearchEngineScore(msRun, paramList); } paramList.Add(param); return true; }
public bool AddSearchEngineScore(MsRun msRun, CVParam param) { if (param == null){ return false; } SplitList<Param> searchparams = getSearchEngineScore(msRun); if (searchparams == null){ searchparams = new SplitList<Param>(MZTabConstants.BAR); SetSearchEngineScore(msRun, searchparams); } searchparams.Add(param); return true; }
private void addProteinValue() { MsRun msRun1 = new MsRun(1); MsRun msRun2 = new MsRun(2); Assay assay1 = new Assay(1); Assay assay2 = new Assay(2); StudyVariable studyVariable1 = new StudyVariable(1); MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Protein_Header); factory.AddOptionalColumn(ProteinColumn.SEARCH_ENGINE_SCORE, msRun1); factory.AddOptionalColumn(ProteinColumn.NUM_PSMS, msRun1); factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_DISTINCT, msRun1); factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_UNIQUE, msRun1); factory.AddOptionalColumn(ProteinColumn.NUM_PSMS, msRun2); factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_DISTINCT, msRun2); factory.AddAbundanceOptionalColumn(assay1); factory.AddAbundanceOptionalColumn(studyVariable1); factory.AddAbundanceOptionalColumn(assay2); factory.AddOptionalColumn(assay1, "my_value", typeof (string)); CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null); factory.AddOptionalColumn(param, typeof (string)); Console.WriteLine(factory); Protein protein = new Protein(factory); // set stable columns data. protein.Accession = "P12345"; protein.Description = "Aspartate aminotransferase, mitochondrial"; protein.SetTaxid("10116"); protein.Species = "Rattus norvegicus (Rat)"; protein.Database = "UniProtKB"; protein.DatabaseVersion = "2011_11"; protein.SetSearchEngine("[MS,MS:1001207,Mascot,]"); protein.AddSearchEngine("[MS,MS:1001208,Sequest,]"); protein.SetBestSearchEngineScore("[MS,MS:1001171,Mascot score,50]|[MS,MS:1001155,Sequest:xcorr,2]"); protein.Reliability = Reliability.High; protein.SetAmbiguityMembers("P12347,P12348"); protein.SetModifications("3|4|8-MOD:00412, 3|4|8-MOD:00412"); protein.SetURI("http://www.ebi.ac.uk/pride/url/to/P12345"); protein.SetGOTerms("GO:0006457|GO:0005759|GO:0005886|GO:0004069"); protein.SetProteinCoverage("0.4"); Console.WriteLine(protein); // set optional columns which have stable order. protein.setSearchEngineScore(msRun1, "[MS,MS:1001171,Mascot score,50]|[MS,MS:1001155,Sequest:xcorr,2]"); protein.setNumPSMs(msRun1, 4); protein.setNumPSMs(msRun2, 2); protein.setNumPeptidesDistinct(msRun1, 3); protein.setNumPeptidesUnique(msRun1, 2); Console.WriteLine(protein); // set abundance columns protein.setAbundanceColumn(assay1, "0.4"); protein.setAbundanceColumn(assay2, "0.2"); protein.setAbundanceColumn(studyVariable1, "0.4"); protein.setAbundanceStdevColumn(studyVariable1, "0.3"); protein.setAbundanceStdErrorColumn(studyVariable1, "0.2"); Console.WriteLine(protein); // set user defined optional columns protein.setOptionColumn(assay1, "my_value", "My value about assay[1]"); protein.setOptionColumn(param, "TOM value"); Console.WriteLine(protein); }
private void addSmallMoleculeValue() { MsRun msRun1 = new MsRun(1); Assay assay1 = new Assay(1); Assay assay2 = new Assay(2); StudyVariable studyVariable1 = new StudyVariable(1); MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Small_Molecule); factory.AddAbundanceOptionalColumn(assay1); factory.AddAbundanceOptionalColumn(studyVariable1); factory.AddAbundanceOptionalColumn(assay2); factory.AddOptionalColumn(msRun1, "my_value", typeof (string)); CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null); factory.AddOptionalColumn(param, typeof (string)); Metadata metadata = new Metadata(); metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file")); Console.WriteLine(factory); /*TODO: SmallMolecule sm = new SmallMolecule(factory, metadata); sm.setIdentifier("CID:00027395"); sm.setChemicalFormula("C17H20N4O2"); sm.setSmiles("C1=CC=C(C=C1)CCNC(=O)CCNNC(=O)C2=CC=NC=C2"); sm.setInchiKey("QXBMEGUKVLFJAM-UHFFFAOYSA-N"); sm.setDescription("N-(2-phenylethyl)-3-[2-(pyridine-4-carbonyl)hydrazinyl]propanamide"); sm.setExpMassToCharge("1234.4"); sm.setCalcMassToCharge("1234.5"); sm.setCharge("2"); sm.setRetentionTime("10.2|11.5"); sm.setTaxid("10116"); sm.setSpecies("Rattus norvegicus (Rat)"); sm.setDatabase("UniProtKB"); sm.setDatabaseVersion("2011_11"); sm.setReliability("2"); sm.setURI("http://www.ebi.ac.uk/pride/link/to/identification"); sm.setSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9"); sm.setSearchEngine("[MS, MS:1001477, SpectraST,]"); sm.setBestSearchEngineScore("[MS, MS:1001419, SpectraST:discriminant score F, 0.7]"); sm.setModifications("CHEMMOD:+Na-H"); Console.WriteLine(sm);*/ }
private void addPSMValue() { Assay assay1 = new Assay(1); MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.PSM_Header); factory.AddOptionalColumn(assay1, "my_value", typeof (string)); CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null); factory.AddOptionalColumn(param, typeof (string)); Metadata metadata = new Metadata(); metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file")); Console.WriteLine(factory); PSM psm = new PSM(factory, metadata); psm.Sequence = "KVPQVSTPTLVEVSR"; psm.SetPSM_ID("1"); psm.Accession = "P02768"; psm.Unique = MZBoolean.False; psm.Database = "UniProtKB"; psm.DatabaseVersion = "2011_11"; psm.setSearchEngine("[MS,MS:1001207,Mascot,]|[MS,MS:1001208,Sequest,]"); psm.setSearchEngineScore("[MS,MS:1001155,Sequest:xcorr,2]"); psm.setReliability("3"); psm.setModifications("CHEMMOD:+159.93"); psm.AddRetentionTime(10.2); psm.Charge = new Integer(2); psm.SetExpMassToCharge("1234.4"); psm.SetCalcMassToCharge("123.4"); psm.SetUri("http://www.ebi.ac.uk/pride/link/to/peptide"); psm.SetSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9"); psm.Pre = "K"; psm.Post = "D"; psm.Start = "45"; psm.End = "57"; Console.WriteLine(psm); }
public void AddPosition(int id, CVParam param) { _positionMap.Add(id, param); }
/** * Add {@link CVParamOptionColumn} followed by ms_run into {@link #optionalColumnMapping} and {@link #columnMapping}. * The header like: opt_ms_run[1]_cv_{accession}_{parameter name} * * @param msRun SHOULD NOT empty. * @param param SHOULD NOT empty. * @param columnType SHOULD NOT empty. */ public string AddOptionalColumn(MsRun msRun, CVParam param, Type columnType) { MZTabColumn column = new CVParamOptionColumn(msRun, param, columnType, ParseColumnOrder(columnMapping.Last().Key)); return AddOptionColumn(column); }
/** * Add {@link CVParamOptionColumn} followed by study variable into {@link #optionalColumnMapping} and {@link #columnMapping}. * The header like: opt_study_variable[1]_cv_{accession}_{parameter name} * * @param studyVariable SHOULD NOT empty. * @param param SHOULD NOT empty. * @param columnType SHOULD NOT empty. */ public string AddOptionalColumn(StudyVariable studyVariable, CVParam param, Type columnType) { MZTabColumn column = new CVParamOptionColumn(studyVariable, param, columnType, ParseColumnOrder(columnMapping.Last().Key)); return AddOptionColumn(column); }
/** * Some {@link CVParamOptionColumn}, their data type have defined. Currently, we provide two {@link CVParam} * which defined in the mzTab specification. One is "emPAI value" (MS:1001905), data type is Double; * another is "decoy peptide" (MS:1002217), the data type is Boolean (0/1). Besides them, "opt_" start optional * column data type is string. * * @see #checkOptColumnName(string) */ private Type getDataType(CVParam param) { Type dataType; if (param == null){ dataType = typeof (string); } else if (param.Accession.Equals("MS:1001905")){ dataType = typeof (double); } else if (param.Accession.Equals("MS:1002217")){ dataType = typeof (MZBoolean); } else{ dataType = typeof (string); } return dataType; }
public CVParamOptionColumn(IndexedElement element, CVParam param, System.Type columnType, int offset) : base(element, CV + param.Accession + "_" + param.Name.Replace(" ", "_"), columnType, offset) { this.param = param; }